Contents

1 Cellranger Illumina profiling (190c)

## [1] 27998   190
## [1] 27998   186

## [1] 2000

## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
## 
## Number of nodes: 186
## Number of edges: 4045
## 
## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 0.7919
## Number of communities: 4
## Elapsed time: 0 seconds

2 Cellranger Illumina profiling (951c)

## [1] 27998   951
## [1] 27998   935

## [1] 2000

## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
## 
## Number of nodes: 935
## Number of edges: 25447
## 
## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 0.8540
## Number of communities: 9
## Elapsed time: 0 seconds

3 Adding Nanopore data (ISOG/ISO)

4 Integration (RNA)

## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
## 
## Number of nodes: 1121
## Number of edges: 31187
## 
## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 0.8374
## Number of communities: 10
## Elapsed time: 0 seconds

5 Gene Markers Heatmap

6 Correlation between clusters

7 Clusters re-labelling, saving .rds file

8 Dotplot

9 Gene markers

10 Heatmap

11 Dotplot isoforms

12 Session Info

sessionInfo()
## R version 3.5.2 (2018-12-20)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Debian GNU/Linux buster/sid
## 
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.3.5.so
## 
## locale:
##  [1] LC_CTYPE=fr_FR.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=fr_FR.UTF-8        LC_COLLATE=fr_FR.UTF-8    
##  [5] LC_MONETARY=fr_FR.UTF-8    LC_MESSAGES=fr_FR.UTF-8   
##  [7] LC_PAPER=fr_FR.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] bindrcpp_0.2.2      DoubletFinder_2.0.1 metap_1.1          
##  [4] cowplot_0.9.4       ggrepel_0.8.0       xtable_1.8-3       
##  [7] knitr_1.21          RColorBrewer_1.1-2  forcats_0.4.0      
## [10] stringr_1.3.1       purrr_0.3.0         readr_1.3.1        
## [13] tidyr_0.8.2         tibble_2.0.1        ggplot2_3.1.0      
## [16] tidyverse_1.2.1     pheatmap_1.0.12     dplyr_0.7.8        
## [19] Seurat_3.0.0.9000   BiocStyle_2.10.0   
## 
## loaded via a namespace (and not attached):
##  [1] Rtsne_0.15          colorspace_1.4-0    ggridges_0.5.1     
##  [4] rstudioapi_0.10     listenv_0.7.0       npsurv_0.4-0       
##  [7] lubridate_1.7.4     xml2_1.2.0          codetools_0.2-16   
## [10] splines_3.5.2       R.methodsS3_1.7.1   lsei_1.2-0         
## [13] jsonlite_1.6        broom_0.5.1         ica_1.0-2          
## [16] cluster_2.0.7-1     png_0.1-7           R.oo_1.22.0        
## [19] BiocManager_1.30.4  compiler_3.5.2      httr_1.4.0         
## [22] backports_1.1.3     assertthat_0.2.0    Matrix_1.2-15      
## [25] lazyeval_0.2.1      cli_1.0.1           htmltools_0.3.6    
## [28] tools_3.5.2         rsvd_1.0.0          igraph_1.2.4       
## [31] gtable_0.2.0        glue_1.3.0          RANN_2.6.1         
## [34] Rcpp_1.0.0          cellranger_1.1.0    gdata_2.18.0       
## [37] ape_5.3             nlme_3.1-137        gbRd_0.4-11        
## [40] lmtest_0.9-36       xfun_0.4            globals_0.12.4     
## [43] rvest_0.3.2         irlba_2.3.3         gtools_3.8.1       
## [46] future_1.12.0       MASS_7.3-51.1       zoo_1.8-5          
## [49] scales_1.0.0        hms_0.4.2           parallel_3.5.2     
## [52] yaml_2.2.0          reticulate_1.11.1   pbapply_1.4-0      
## [55] stringi_1.2.4       caTools_1.17.1.1    bibtex_0.4.2       
## [58] Rdpack_0.10-1       SDMTools_1.1-221    rlang_0.3.1        
## [61] pkgconfig_2.0.2     bitops_1.0-6        evaluate_0.12      
## [64] lattice_0.20-38     ROCR_1.0-7          bindr_0.1.1        
## [67] htmlwidgets_1.3     labeling_0.3        tidyselect_0.2.5   
## [70] plyr_1.8.4          magrittr_1.5        bookdown_0.9       
## [73] R6_2.3.0            gplots_3.0.1.1      generics_0.0.2     
## [76] pillar_1.3.1        haven_2.1.0         withr_2.1.2        
## [79] fitdistrplus_1.0-14 survival_2.43-3     future.apply_1.2.0 
## [82] tsne_0.1-3          modelr_0.1.4        crayon_1.3.4       
## [85] KernSmooth_2.23-15  plotly_4.8.0        rmarkdown_1.11     
## [88] grid_3.5.2          readxl_1.3.1        data.table_1.12.0  
## [91] digest_0.6.18       R.utils_2.8.0       munsell_0.5.0      
## [94] viridisLite_0.3.0